lesson4/answers/part4/featureCounts.cwl

   1 cwlVersion: v1.2
   2 class: CommandLineTool
   3
   4 ### 4. Combining results
   5 inputs:
   6   gtf: File
   7   counts_input_bam:
   8    - File
   9    - File[]
  10
  11 baseCommand: featureCounts
  12
  13 arguments: [-T, $(runtime.cores),
  14             -a, $(inputs.gtf),
  15             -o, featurecounts.tsv,
  16             $(inputs.counts_input_bam)]
  17
  18 outputs:
  19   featurecounts:
  20     type: File
  21     outputBinding:
  22       glob: featurecounts.tsv
  23
  24 hints:
  25   DockerRequirement:
  26     dockerPull: quay.io/biocontainers/subread:1.5.0p3--0